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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs200980371

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:65366003 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000008 (1/121112, ExAC)
C=0.0003 (2/6404, 1000G_30x)
C=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EPHA5 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
ExAC Global Study-wide 121112 T=0.999992 C=0.000008
ExAC Europe Sub 73196 T=1.00000 C=0.00000
ExAC Asian Sub 25122 T=1.00000 C=0.00000
ExAC American Sub 11500 T=1.00000 C=0.00000
ExAC African Sub 10390 T=0.99990 C=0.00010
ExAC Other Sub 904 T=1.000 C=0.000
1000Genomes_30x Global Study-wide 6404 T=0.9997 C=0.0003
1000Genomes_30x African Sub 1786 T=0.9989 C=0.0011
1000Genomes_30x Europe Sub 1266 T=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 T=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=1.000 C=0.000
1000Genomes Global Study-wide 5008 T=0.9998 C=0.0002
1000Genomes African Sub 1322 T=0.9992 C=0.0008
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=1.000 C=0.000
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 4 NC_000004.12:g.65366003T>A
GRCh38.p14 chr 4 NC_000004.12:g.65366003T>C
GRCh37.p13 chr 4 NC_000004.11:g.66231721T>A
GRCh37.p13 chr 4 NC_000004.11:g.66231721T>C
Gene: EPHA5, EPH receptor A5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPHA5 transcript variant 1 NM_004439.8:c.1979A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform a NP_004430.4:p.Asn660Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant 1 NM_004439.8:c.1979A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform a NP_004430.4:p.Asn660Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant 5 NM_001281767.3:c.1982A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform e NP_001268696.1:p.Asn661Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant 5 NM_001281767.3:c.1982A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform e NP_001268696.1:p.Asn661Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant 2 NM_182472.5:c.1913A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform b NP_872272.2:p.Asn638Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant 2 NM_182472.5:c.1913A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform b NP_872272.2:p.Asn638Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant 4 NM_001281766.3:c.1916A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform d NP_001268695.1:p.Asn639Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant 4 NM_001281766.3:c.1916A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform d NP_001268695.1:p.Asn639Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant 3 NM_001281765.3:c.1982A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform c NP_001268694.1:p.Asn661Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant 3 NM_001281765.3:c.1982A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform c NP_001268694.1:p.Asn661Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant 6 NM_001318761.2:c.1775A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform f NP_001305690.1:p.Asn592Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant 6 NM_001318761.2:c.1775A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform f NP_001305690.1:p.Asn592Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X1 XM_011531735.4:c.1646A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X1 XP_011530037.1:p.Asn549Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X1 XM_011531735.4:c.1646A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X1 XP_011530037.1:p.Asn549Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X2 XM_017007878.3:c.1580A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X2 XP_016863367.1:p.Asn527Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X2 XM_017007878.3:c.1580A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X2 XP_016863367.1:p.Asn527Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X3 XM_047449762.1:c.1577A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X3 XP_047305718.1:p.Asn526Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X3 XM_047449762.1:c.1577A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X3 XP_047305718.1:p.Asn526Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X4 XM_005265653.5:c.1490A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X4 XP_005265710.1:p.Asn497Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X4 XM_005265653.5:c.1490A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X4 XP_005265710.1:p.Asn497Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X5 XM_047449763.1:c.1487A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X5 XP_047305719.1:p.Asn496Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X5 XM_047449763.1:c.1487A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X5 XP_047305719.1:p.Asn496Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X6 XM_017007880.3:c.1424A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X6 XP_016863369.1:p.Asn475Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X6 XM_017007880.3:c.1424A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X6 XP_016863369.1:p.Asn475Ser N (Asn) > S (Ser) Missense Variant
EPHA5 transcript variant X7 XM_017007881.3:c.1421A>T N [AAT] > I [ATT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X7 XP_016863370.1:p.Asn474Ile N (Asn) > I (Ile) Missense Variant
EPHA5 transcript variant X7 XM_017007881.3:c.1421A>G N [AAT] > S [AGT] Coding Sequence Variant
ephrin type-A receptor 5 isoform X7 XP_016863370.1:p.Asn474Ser N (Asn) > S (Ser) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= A C
GRCh38.p14 chr 4 NC_000004.12:g.65366003= NC_000004.12:g.65366003T>A NC_000004.12:g.65366003T>C
GRCh37.p13 chr 4 NC_000004.11:g.66231721= NC_000004.11:g.66231721T>A NC_000004.11:g.66231721T>C
EPHA5 transcript variant 1 NM_004439.8:c.1979= NM_004439.8:c.1979A>T NM_004439.8:c.1979A>G
EPHA5 transcript variant 1 NM_004439.7:c.1979= NM_004439.7:c.1979A>T NM_004439.7:c.1979A>G
EPHA5 transcript variant 1 NM_004439.6:c.1979= NM_004439.6:c.1979A>T NM_004439.6:c.1979A>G
EPHA5 transcript variant 1 NM_004439.5:c.1979= NM_004439.5:c.1979A>T NM_004439.5:c.1979A>G
EPHA5 transcript variant 2 NM_182472.5:c.1913= NM_182472.5:c.1913A>T NM_182472.5:c.1913A>G
EPHA5 transcript variant 2 NM_182472.4:c.1913= NM_182472.4:c.1913A>T NM_182472.4:c.1913A>G
EPHA5 transcript variant 2 NM_182472.3:c.1913= NM_182472.3:c.1913A>T NM_182472.3:c.1913A>G
EPHA5 transcript variant 2 NM_182472.2:c.1913= NM_182472.2:c.1913A>T NM_182472.2:c.1913A>G
EPHA5 transcript variant X4 XM_005265653.5:c.1490= XM_005265653.5:c.1490A>T XM_005265653.5:c.1490A>G
EPHA5 transcript variant X3 XM_005265653.4:c.1490= XM_005265653.4:c.1490A>T XM_005265653.4:c.1490A>G
EPHA5 transcript variant X3 XM_005265653.3:c.1490= XM_005265653.3:c.1490A>T XM_005265653.3:c.1490A>G
EPHA5 transcript variant X4 XM_005265653.2:c.1490= XM_005265653.2:c.1490A>T XM_005265653.2:c.1490A>G
EPHA5 transcript variant X4 XM_005265653.1:c.1490= XM_005265653.1:c.1490A>T XM_005265653.1:c.1490A>G
EPHA5 transcript variant X1 XM_011531735.4:c.1646= XM_011531735.4:c.1646A>T XM_011531735.4:c.1646A>G
EPHA5 transcript variant X1 XM_011531735.3:c.1646= XM_011531735.3:c.1646A>T XM_011531735.3:c.1646A>G
EPHA5 transcript variant X1 XM_011531735.2:c.1646= XM_011531735.2:c.1646A>T XM_011531735.2:c.1646A>G
EPHA5 transcript variant X3 XM_011531735.1:c.1646= XM_011531735.1:c.1646A>T XM_011531735.1:c.1646A>G
EPHA5 transcript variant 3 NM_001281765.3:c.1982= NM_001281765.3:c.1982A>T NM_001281765.3:c.1982A>G
EPHA5 transcript variant 3 NM_001281765.2:c.1982= NM_001281765.2:c.1982A>T NM_001281765.2:c.1982A>G
EPHA5 transcript variant 3 NM_001281765.1:c.1982= NM_001281765.1:c.1982A>T NM_001281765.1:c.1982A>G
EPHA5 transcript variant 4 NM_001281766.3:c.1916= NM_001281766.3:c.1916A>T NM_001281766.3:c.1916A>G
EPHA5 transcript variant 4 NM_001281766.2:c.1916= NM_001281766.2:c.1916A>T NM_001281766.2:c.1916A>G
EPHA5 transcript variant 4 NM_001281766.1:c.1916= NM_001281766.1:c.1916A>T NM_001281766.1:c.1916A>G
EPHA5 transcript variant X2 XM_017007878.3:c.1580= XM_017007878.3:c.1580A>T XM_017007878.3:c.1580A>G
EPHA5 transcript variant X2 XM_017007878.2:c.1580= XM_017007878.2:c.1580A>T XM_017007878.2:c.1580A>G
EPHA5 transcript variant X2 XM_017007878.1:c.1580= XM_017007878.1:c.1580A>T XM_017007878.1:c.1580A>G
EPHA5 transcript variant X6 XM_017007880.3:c.1424= XM_017007880.3:c.1424A>T XM_017007880.3:c.1424A>G
EPHA5 transcript variant X5 XM_017007880.2:c.1424= XM_017007880.2:c.1424A>T XM_017007880.2:c.1424A>G
EPHA5 transcript variant X5 XM_017007880.1:c.1424= XM_017007880.1:c.1424A>T XM_017007880.1:c.1424A>G
EPHA5 transcript variant 5 NM_001281767.3:c.1982= NM_001281767.3:c.1982A>T NM_001281767.3:c.1982A>G
EPHA5 transcript variant 5 NM_001281767.2:c.1982= NM_001281767.2:c.1982A>T NM_001281767.2:c.1982A>G
EPHA5 transcript variant 5 NM_001281767.1:c.1982= NM_001281767.1:c.1982A>T NM_001281767.1:c.1982A>G
EPHA5 transcript variant X7 XM_017007881.3:c.1421= XM_017007881.3:c.1421A>T XM_017007881.3:c.1421A>G
EPHA5 transcript variant X6 XM_017007881.2:c.1421= XM_017007881.2:c.1421A>T XM_017007881.2:c.1421A>G
EPHA5 transcript variant X6 XM_017007881.1:c.1421= XM_017007881.1:c.1421A>T XM_017007881.1:c.1421A>G
EPHA5 transcript variant 6 NM_001318761.2:c.1775= NM_001318761.2:c.1775A>T NM_001318761.2:c.1775A>G
EPHA5 transcript variant 6 NM_001318761.1:c.1775= NM_001318761.1:c.1775A>T NM_001318761.1:c.1775A>G
EPHA5 transcript variant X3 XM_047449762.1:c.1577= XM_047449762.1:c.1577A>T XM_047449762.1:c.1577A>G
EPHA5 transcript variant X5 XM_047449763.1:c.1487= XM_047449763.1:c.1487A>T XM_047449763.1:c.1487A>G
ephrin type-A receptor 5 isoform a NP_004430.4:p.Asn660= NP_004430.4:p.Asn660Ile NP_004430.4:p.Asn660Ser
ephrin type-A receptor 5 isoform b NP_872272.2:p.Asn638= NP_872272.2:p.Asn638Ile NP_872272.2:p.Asn638Ser
ephrin type-A receptor 5 isoform X4 XP_005265710.1:p.Asn497= XP_005265710.1:p.Asn497Ile XP_005265710.1:p.Asn497Ser
ephrin type-A receptor 5 isoform X1 XP_011530037.1:p.Asn549= XP_011530037.1:p.Asn549Ile XP_011530037.1:p.Asn549Ser
ephrin type-A receptor 5 isoform c NP_001268694.1:p.Asn661= NP_001268694.1:p.Asn661Ile NP_001268694.1:p.Asn661Ser
ephrin type-A receptor 5 isoform d NP_001268695.1:p.Asn639= NP_001268695.1:p.Asn639Ile NP_001268695.1:p.Asn639Ser
ephrin type-A receptor 5 isoform X2 XP_016863367.1:p.Asn527= XP_016863367.1:p.Asn527Ile XP_016863367.1:p.Asn527Ser
ephrin type-A receptor 5 isoform X6 XP_016863369.1:p.Asn475= XP_016863369.1:p.Asn475Ile XP_016863369.1:p.Asn475Ser
ephrin type-A receptor 5 isoform e NP_001268696.1:p.Asn661= NP_001268696.1:p.Asn661Ile NP_001268696.1:p.Asn661Ser
ephrin type-A receptor 5 isoform X7 XP_016863370.1:p.Asn474= XP_016863370.1:p.Asn474Ile XP_016863370.1:p.Asn474Ser
ephrin type-A receptor 5 isoform f NP_001305690.1:p.Asn592= NP_001305690.1:p.Asn592Ile NP_001305690.1:p.Asn592Ser
ephrin type-A receptor 5 isoform X3 XP_047305718.1:p.Asn526= XP_047305718.1:p.Asn526Ile XP_047305718.1:p.Asn526Ser
ephrin type-A receptor 5 isoform X5 XP_047305719.1:p.Asn496= XP_047305719.1:p.Asn496Ile XP_047305719.1:p.Asn496Ser
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

10 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488787114 May 04, 2012 (137)
2 1000GENOMES ss1310019925 Aug 21, 2014 (142)
3 EVA_EXAC ss1687506721 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2263466627 Dec 20, 2016 (150)
5 GNOMAD ss2734530845 Nov 08, 2017 (151)
6 1000G_HIGH_COVERAGE ss5259452528 Oct 17, 2022 (156)
7 EVA ss5349457649 Oct 17, 2022 (156)
8 1000G_HIGH_COVERAGE ss5540665625 Oct 17, 2022 (156)
9 EVA ss5863721240 Oct 17, 2022 (156)
10 EVA ss5935712345 Oct 17, 2022 (156)
11 1000Genomes NC_000004.11 - 66231721 Oct 12, 2018 (152)
12 1000Genomes_30x NC_000004.12 - 65366003 Oct 17, 2022 (156)
13 ExAC NC_000004.11 - 66231721 Oct 12, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss5935712345 NC_000004.11:66231720:T:A NC_000004.12:65366002:T:A
21425323, 7472015, ss488787114, ss1310019925, ss1687506721, ss2734530845, ss5349457649, ss5935712345 NC_000004.11:66231720:T:C NC_000004.12:65366002:T:C (self)
28191560, ss2263466627, ss5259452528, ss5540665625, ss5863721240 NC_000004.12:65366002:T:C NC_000004.12:65366002:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs200980371

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07